A Solid-State Nanopore microRNA Quantification Platform

MicroRNA (miRNA) profiling in liquid biopsy and single-cell assays by the current microarray, digital PCR and rtPCR technologies are plagued with false positives and negatives, particularly at low copy numbers. A main reason for such inaccuracies is that these technologies are not sufficiently selective for different miRNAs that differ by only a few bases and whose dissociation constants for primer/probe hybridization are nearly identical (Egatz et al,Biomicrofluidics, 10: 032902(2016)).

We report a new highly selective (PCR-free) solid-state nanopore miRNA quantification platform for liquid biopsy and single-cell assays. A single ion-track nanopore in a PET membrane is asymmetrically etched into a conic geometry and is coated with a high-permittivity dielectric layer by Atomic Layer Deposition (Yan et al, J Chem Phys, 138: 044706(2013)). The surface modified conicnanopore allows for high throughput molecular translocation (100 Hz vs 1 Hz for protein nanopores) and selective delay of single-stranded (ss) nucleic acids compared to their hybridized double-stranded (ds) duplex (mean translocation time of 100 ms vs 1 ms with 5% overlap in the two distributions). The delay is due to enhanced van der Waal attraction between exposed rings of the ss-nucleic acids, withdelocalized electrons, with the high-permittivity coating. Individual translocation events can be recorded for a mixture of ss- and ds-nucleic acids numbering between 100 to 100,000. Whether thetranslocating molecule of each event is an ss miRNA or its ds duplex can be discerned with 95% confidence.